Merge branch 'release-v2.0.0' into development

.gitignore

@@ -80,3 +80,6 @@ virt3/
 
 # PyCharm
 .idea/
+
+# MyPy
+/.mypy_cache/

CONTRIBUTORS.md

@@ -1,16 +1,15 @@
-Brandon DeMello 
- - Initial Developer for the ISOBAR model
+# Contributors to PyPWA (in Chronological Order)
 
-Josh Pond 
- - Added batch farm submission 
- - made initial General Shell
+## PyPWA Staff:
+ - Carlos Salgado <https://github.com/cwsalgado>
+ - Will Phelps <https://github.com/wphelps>
+ - Brandon DeMello <https://github.com/bdell>
+ - Stephanie Bramlett <https://github.com/skbramlett>
+ - Josh Pond <https://github.com/JTPond>
+ - Mark Jones <markjonestx@live.com> <https://github.com/Markjonestx>
+ - LaRay Hare <https://github.com/lmhare>
 
-Stephanie Bramlett
- - Wrote vector libraries
-
-Mark Jones
- - Added setup.py for package
- - Added plugin loader
- - Wrote PyFit and PySimulate
- - Added logging
+High School Interns:
 
+ - Ryan Wright <https://github.com/painballking>
+   - Ran Amplitude benchmarks on the XeonPhi

PyPWA/builtin_plugins/minuit/minimization.py

@@ -45,7 +45,7 @@
 
 class _ParserObject(internals.OptimizerOptionParser):
 
-    multiplier = -1
+    MULTIPLIER = -1
 
     def __init__(self, parameters):
         self._parameters = parameters

PyPWA/builtin_plugins/nestle/_setup.py

@@ -22,13 +22,14 @@
 """
 
 import logging
+from typing import Callable
 
-import typing
+import numpy
 
 from PyPWA import AUTHOR, VERSION
 from PyPWA.builtin_plugins.nestle import nested
-from PyPWA.core.configurator import options
 from PyPWA.core.configurator import option_tools
+from PyPWA.core.configurator import options
 
 __credits__ = ["Mark Jones"]
 __author__ = AUTHOR
@@ -37,15 +38,16 @@
 
 class NestleSetup(options.Setup):
 
-    __logger = logging.getLogger("NestleSetup." + __name__)
-    __loader = nested.LoadPrior()
-
-    __interface = None  # type: nested.NestledSampling()
-    __options = None  # type: option_tools.CommandOptions
-    __prior = None  # type: typing.Any
+    __LOGGER = logging.getLogger(__name__ + ".NestleSetup")
 
     def __init__(self, options_object):
+        # type: (option_tools.CommandOptions) -> None
         self.__options = options_object
+        self.__loader = nested.LoadPrior()
+
+        self.__prior = None  # type: Callable[[numpy.ndarray], numpy.ndarray]
+        self.__minimizer = None  # type: nested.NestledSampling
+
         self.__load_prior()
         self.__set_minimizer()
 
@@ -56,7 +58,7 @@ def __load_prior(self):
         self.__prior = self.__loader.prior
 
     def __set_minimizer(self):
-        self.__interface = nested.NestledSampling(
+        self.__minimizer = nested.NestledSampling(
             self.__prior, self.__options.ndim, self.__options.npoints,
             self.__options.method, self.__options.update_interval,
             self.__options.npdim, self.__options.maxiter,
@@ -65,14 +67,16 @@ def __set_minimizer(self):
         )
 
     def return_interface(self):
-        return self.__interface
+        # type: () -> nested.NestledSampling
+        return self.__minimizer
 
 
 class NestlePriorFunction(options.FileBuilder):
     imports = set()
     functions = [
         """
 def prior(x):
+    # type: Callable[[numpy.ndarray], numpy.ndarray]
     # For information about how to use nestle's prior function, please read
     # nestle's documentation at: http://kylebarbary.com/nestle/index.html
     return x

PyPWA/builtin_plugins/process/_processing.py

@@ -59,7 +59,7 @@ def __init__(self, index, kernel, communicator, level, file):
         self.__logging_level = level
         self.__logging_file = file
         self._kernel = kernel
-        self._kernel.processor_id = index
+        self._kernel.PROCESS_ID = index
         self._communicator = communicator
 
     def run(self):
@@ -73,14 +73,14 @@ def run(self):
         self.__setup_logger()
         self.__set_logger()
         self.__logger.debug(
-            "Starting logging in proc index %d" % self._kernel.processor_id
+            "Starting logging in proc index %d" % self._kernel.PROCESS_ID
         )
         self._kernel.setup()
         while True:
             value = self._communicator.receive()
             if isinstance(value, str) and value == "DIE":
                 self.__logger.debug(
-                    "Shutting down %d" % self._kernel.processor_id
+                    "Shutting down %d" % self._kernel.PROCESS_ID
                 )
                 break
             else:
@@ -121,7 +121,7 @@ def __init__(self, index, single_kernel, communicator, level, file):
         self.__logging_level = level
         self.__logging_file = file
         self._kernel = single_kernel
-        self._kernel.processor_id = index
+        self._kernel.PROCESS_ID = index
         self._communicator = communicator
 
     def run(self):
@@ -136,7 +136,7 @@ def run(self):
         self.__set_logger()
         self._kernel.setup()
         self.__logger.debug(
-            "Starting logging in proc index %d" % self._kernel.processor_id
+            "Starting logging in proc index %d" % self._kernel.PROCESS_ID
         )
         self._communicator.send(self._kernel.process())
         return 0

PyPWA/builtin_plugins/process/foreman.py

@@ -58,7 +58,6 @@ def __init__(self, interface_kernel, process_com, processes, duplex):
                 processing processes.
         """
         self._logger = logging.getLogger(__name__)
-        self._logger.addHandler(logging.NullHandler())
 
         self._com = process_com
         self._interface_kernel = interface_kernel
@@ -157,7 +156,6 @@ def __init__(
         self._interface_template = False
 
         self._logger = logging.getLogger(__name__)
-        self._logger.addHandler(logging.NullHandler())
 
         self._number_of_processes = number_of_processes
 
@@ -187,7 +185,7 @@ def main_options(self, data, process_template, interface_template):
             process_template, process_data
         )
 
-        self._duplex = interface_template.is_duplex
+        self._duplex = interface_template.IS_DUPLEX
         self._interface_template = interface_template
 
         self._interface = self._build()

PyPWA/core/shared/interfaces/internals.py

@@ -49,6 +49,9 @@
 """
 
 import enum
+from typing import Any, List
+from typing import Optional as Opt
+
 import numpy
 
 from PyPWA import AUTHOR, VERSION
@@ -61,6 +64,7 @@
 class Reader(object):
 
     def next(self):
+        # type: () -> numpy.ndarray
         """
         Called to get the next event from the reader.
         
@@ -82,6 +86,7 @@ def __exit__(self, *args):
         self.close()
 
     def close(self):
+        # type: () -> None
         """
         Should close any open objects or streams.
         """
@@ -91,6 +96,7 @@ def close(self):
 class Writer(object):
 
     def write(self, data):
+        # type: (numpy.ndarray) -> None
         """
         Should write the received event to the stream.
         
@@ -105,6 +111,7 @@ def __exit__(self, *args):
         self.close()
 
     def close(self):
+        # type: () -> None
         """
         Should close the stream and any open streams or objects.
         """
@@ -114,6 +121,7 @@ def close(self):
 class ProcessInterface(object):
 
     def run(self, *args):
+        # type: (*Any) -> Any
         """
         This function will start the processing of the processes, whatever was
         passed through the kernel will be started with this method.
@@ -125,6 +133,7 @@ def run(self, *args):
 
     @property
     def previous_value(self):
+        # type: () -> Any
         """
         The previous value received from the kernel interface.
         
@@ -133,6 +142,7 @@ def previous_value(self):
         raise NotImplementedError
 
     def stop(self, force=False):
+        # type: (Opt[bool]) -> None
         """
         Should stop all process, threads, etc, that are being used to 
         calculate.
@@ -144,6 +154,7 @@ def stop(self, force=False):
 
     @property
     def is_alive(self):
+        # type: () -> bool
         """
         Should return whether the children are still alive or have been 
         shutdown.
@@ -157,16 +168,18 @@ def is_alive(self):
 class Kernel(object):
 
     # process_id should be set by the Kernel Processing plugin.
-    processor_id = None  # type: int
+    PROCESS_ID = None  # type: int
 
     def setup(self):
+        # type: () -> None
         """
         Anything that should be setup in the thread or process should be 
         put here, this will be called only once before any calculation begins.
         """
         raise NotImplementedError()
 
     def process(self, data=False):
+        # type: (Opt[Any]) -> Any
         """
         The actual calculation or function of the program, can optionally 
         support values from the main thread / process.
@@ -186,9 +199,10 @@ class KernelInterface(object):
     # its first run; however, if this is true then the kernel will stay
     # running and waiting for a value from the interface indefinitely until
     # they are shutdown manually.
-    is_duplex = False
+    IS_DUPLEX = False
 
     def run(self, communicator, args):
+        # type: (List[Any], Any) -> Any
         """
         The method that will be called to begin the calculation. This is 
         the interface between the kernels and the calling object.
@@ -205,9 +219,10 @@ class OptimizerOptionParser(object):
 
     # A simple multiplier that will be multiplied to the final result of
     # every run call.
-    multiplier = 1
+    MULTIPLIER = 1
 
     def convert(self, passed_value):
+        # type: (Any) -> Any
         """
         This should take any value sent by optimizer and clean up the value 
         to something easier for the user to interact with if possible.